VMD-L Mailing List
From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Sep 23 2009 - 13:13:12 CDT
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Hello,
I have a small molecule that i would like to visualize using VMD, the
molecule is in mol2 format. if i view the molecule the double bond is
shown as a single bond. How can i correct this?
In AMBER i can load the *.lib file but i cannot load the *.lib file into
VMD.
Best,
Taufik
!!index array str
"beg"
!entry.beg.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"C1" "C.2" 0 1 131072 1 6 0.380000
"O11" "O.2" 0 1 131072 2 8 -0.380000
"C2" "C.3" 0 1 131072 3 6 -0.100000
"C21" "C.3" 0 1 131072 4 6 -0.300000
"H211" "H" 0 1 131072 5 1 0.100000
"H212" "H" 0 1 131072 6 1 0.100000
"H213" "H" 0 1 131072 7 1 0.100000
"C22" "C.3" 0 1 131072 8 6 -0.300000
"H221" "H" 0 1 131072 9 1 0.100000
"H222" "H" 0 1 131072 10 1 0.100000
"H223" "H" 0 1 131072 11 1 0.100000
!entry.beg.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"C1" "C.2" 0 -1 0.0
"O11" "O.2" 0 -1 0.0
"C2" "C.3" 0 -1 0.0
"C21" "C.3" 0 -1 0.0
"H211" "H" 0 -1 0.0
"H212" "H" 0 -1 0.0
"H213" "H" 0 -1 0.0
"C22" "C.3" 0 -1 0.0
"H221" "H" 0 -1 0.0
"H222" "H" 0 -1 0.0
"H223" "H" 0 -1 0.0
!entry.beg.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.beg.unit.childsequence single int
2
!entry.beg.unit.connect array int
3
1
!entry.beg.unit.connectivity table int atom1x int atom2x int flags
1 3 1
1 2 2
3 4 1
3 8 1
4 5 1
4 6 1
4 7 1
8 9 1
8 10 1
8 11 1
!entry.beg.unit.hierarchy table str abovetype int abovex str belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
!entry.beg.unit.name single str
"BEG"
!entry.beg.unit.positions table dbl x dbl y dbl z
3.214933 0.278008 -8.099325
2.350808 0.765469 -7.183709
4.591772 0.471138 -7.934938
5.034136 -0.159258 -6.647451
6.018086 -0.024677 -6.530453
4.546759 0.264689 -5.883849
4.831984 -1.138299 -6.669297
4.889342 1.941208 -7.902272
5.872960 2.080402 -7.787925
4.590888 2.360555 -8.759554
4.402031 2.363165 -7.137527
!entry.beg.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
0 0 0 0 0 0
!entry.beg.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
"BEG" 1 12 1 "?" 0
!entry.beg.unit.residuesPdbSequenceNumber array int
0
!entry.beg.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.beg.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
@<TRIPOS>MOLECULE
BEG
11 10 1 0 1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C1 3.214933 0.278008 -8.099325 C.2 1 BEG 0.3800 ****
2 O11 2.350808 0.765469 -7.183709 O.2 1 BEG -0.3800 ****
3 C2 4.591772 0.471138 -7.934938 C.3 1 BEG -0.1000 ****
4 C21 5.034136 -0.159258 -6.647451 C.3 1 BEG -0.3000 ****
5 H211 6.018086 -0.024677 -6.530453 H 1 BEG 0.1000 ****
6 H212 4.546759 0.264689 -5.883849 H 1 BEG 0.1000 ****
7 H213 4.831984 -1.138299 -6.669297 H 1 BEG 0.1000 ****
8 C22 4.889342 1.941208 -7.902272 C.3 1 BEG -0.3000 ****
9 H221 5.872960 2.080402 -7.787925 H 1 BEG 0.1000 ****
10 H222 4.590888 2.360555 -8.759554 H 1 BEG 0.1000 ****
11 H223 4.402031 2.363165 -7.137527 H 1 BEG 0.1000 ****
@<TRIPOS>BOND
1 1 3 1
2 1 2 1
3 3 4 1
4 3 8 1
5 4 5 1
6 4 6 1
7 4 7 1
8 8 9 1
9 8 10 1
10 8 11 1
@<TRIPOS>SUBSTRUCTURE
1 BEG 1 **** 0 **** ****
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